Pockets And Cavities Using Pseudoatoms in Proteins

PACUPP is a Jmol script that fills pockets, cavities, tunnels/channels in proteins with pseudoatoms. PACUPP provides tools to isolate cavities of interest and display their contents, their linings (and list the lining atoms, spreadsheet-ready), entrances (mouths), volumes, shapes, and dimensions. PACUPP adds the pseudoatoms to an output PDB file, which can then be viewed in Jmol with PACUPP commands, or in the software of your choice (e.g. PyMOL, Chimera, VMD, Cn3D, etc.). PACUPP (Jmol) is Java-based, and thus works in Windows, macOS, and linux.
Version 1.0, December 9, 2020.

Proteasome 1PMA.
Pseudoatoms filling cavity: opaque. Protein: traslucent. Cavity detail: moderate; cavity size: large. Processing time: 5 min.

Lysozyme 1LZR.
Pseudoatoms filling catalytic cleft pink, showing inhibitor and water inside. Cavity detail: fine; cavity size: small. Processing time: 2 sec.
PACUPP is copyright 2020 by Eric Martz and is open-source freeware licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
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